RAK8212: Issue with save() freezing up the system

the board can't be restarted by shorting TILT_DOUT to 3.3

That's intentional - you need to restart while shorting TILT_DOUT to 3.3v to boot without loading code.

it worked when we used the really simple code

Ok, so there's some issue with your code by the sound of it. I'd suggest:

• Reset the board
  
• Connect via Bluetooth
  
• Upload your code and save
  
• Type load() on the left-hand side - this will mimic a power on reset. It might be that you see some errors reported.